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<h1><a href="https://archiveofourown.org/works/27750649">It Takes A Ship</a> by <a class='authorlink' href='https://archiveofourown.org/users/hereforthephilindafics/pseuds/hereforthephilindafics'>hereforthephilindafics</a></h1>

<table class="full">

<tr><td><b>Category:</b></td><td>Star Trek: Voyager</td></tr>

<tr><td><b>Genre:</b></td><td>Character Study, Established Relationship, F/M, Fluff and Humor, the ship knows but they think they are being sneaky</td></tr>

<tr><td><b>Language:</b></td><td>English</td></tr>

<tr><td><b>Status:</b></td><td>Completed</td></tr>

<tr><td><b>Published:</b></td><td>2020-11-28</td></tr>

<tr><td><b>Updated:</b></td><td>2020-11-28</td></tr>

<tr><td><b>Packaged:</b></td><td>2021-05-10 20:40:40</td></tr>

<tr><td><b>Rating:</b></td><td>Teen And Up Audiences</td></tr>

<tr><td><b>Warnings:</b></td><td>No Archive Warnings Apply</td></tr>

<tr><td><b>Chapters:</b></td><td>1</td></tr>

<tr><td><b>Words:</b></td><td>2,736</td></tr>

<tr><td><b>Publisher:</b></td><td>archiveofourown.org</td></tr>

<tr><td><b>Story URL:</b></td><td>https://archiveofourown.org/works/27750649</td></tr>

<tr><td><b>Author URL:</b></td><td>https://archiveofourown.org/users/hereforthephilindafics/pseuds/hereforthephilindafics</td></tr>

<tr><td><b>Summary:</b></td><td><div class="userstuff">
              <p>Chakotay and Janeway might think they are being discreet and keeping their relationship secret, but Voyager is a small ship, especially when Tuvok is your Chief of Security.</p><p>Chakotay and Janeway's relationship through the eyes of those who know them best.</p>
            </div></td></tr>

<tr><td><b>Relationships:</b></td><td>Chakotay/Kathryn Janeway</td></tr>

<tr><td><b>Comments:</b></td><td>16</td></tr>

<tr><td><b>Kudos:</b></td><td>83</td></tr>

</table>

<a name="section0001"><h2>It Takes A Ship</h2></a>
<div class="story"><div class="fff_chapter_notes fff_head_notes"><b>Author's Note:</b><blockquote class="userstuff">
      <p>I wrote something similar for Picard/Crusher and really enjoyed it so I decided to do the same for J/C.</p><p>Enjoy!</p>
    </blockquote></div><div class="userstuff module">
    
    <p>Tuvok liked to check the transport logs monthly, even while they were in the Delta Quadrant. It was a routine he had created ever since becoming Chief of Security. Protocol regarding site-to-site transport logs dictated checks needed to be run every three months. Captain Janeway agreed. After the third monthly check of transporter logs, he started understanding why the Captain was so adamant on him running less reports.</p><p>The deleted site-to-site log appeared once every seven days, always on a Saturday, between o-four and o-five hundred hours. The first time, Tuvok assumed it was a glitch, a bad reading that kept being carried over into the files. However, when he accessed the file to delete it, he realized it was a restricted one. It always originated between two locations: Commander Chakotay’s and Captain Janeway’s quarters, alternating in destination.</p><p>Tuvok raised an eyebrow at the screen as he deleted all traces of the transport log. He tried not to speculate on why either of his commanding officers would need to initiate a site-to-site transport weekly and around the same time frame. He did, however, note the incident in his official log.</p><p>After the transport log discrepancy, Tuvok pretended nothing was different, but logical explanation was something a Vulcan could not resist. While reviewing duty roasters, he realized that Captain Janeway and Commander Chakotay had recently changed their duty shift rotations. It so happened that he didn’t work Friday while she didn’t work Saturday, giving them Friday night/early Saturday morning as a window of free time. Not that Tuvok assumed they spent it together.</p><p>Not at first, at least.</p><p>He could, however, no longer ignore the exhaustion that was written all over Commander Chakotay’s face when he walked onto the Bridge every Saturday morning. His uniform was as impeccable as ever, he walked with his back straight and wished everyone a good morning, but Tuvok noticed he slumped the moment he sat in his chair. Lieutenant Paris turned to smirk at him once when Commander Chakotay yawned as he reviewed long range scans.</p><p>And then there was the smell.</p><p>It wasn’t unpleasant per se, but Commander Chakotay smelled different on those Saturday mornings. Tuvok knew he showered before each Bridge shift, but on those days the Commander’s sweat was a little stronger, mixed with a faint scent of roses and peonies, which Tuvok had come to recognize as the Captain’s favorite perfume. The first time he got a whiff of their combined scents Tuvok became momentarily distracted from the scans he was running.</p><p>His theory was further confirmed after he noticed the small changes in the Captain’s behavior toward Commander Chakotay. It was nothing inappropriate or over the top, but she allowed her fingers to linger against the base of his neck a few moments longer when she gripped the Commander’s shoulder. Her eyes followed him as he left the Bridge to join an away team or tend to a problem. His scent lingered in her Ready Room, especially on the couch, which Tuvok made a point to no longer sit on.</p><p>He continued to delete the site-to-site transporter logs between their quarters, confident that his commanding officers were being discrete, and Captain Janeway would go to him if she needed advice.</p><p>~*~</p><p>When Tom started the betting pool on how long it would take the Captain and Commander Chakotay to get together, he had not really expected to see any concrete evidence. It all started as a joke, and a bit of insubordination toward two commanding officers he did not care about at that time or know well. If he could go back and not create the pool, Paris would do so in a heartbeat. He had to admit it was entertaining, however. There were long stretches of time where the pool was quiet, like no one even remembered they had bet anything on the two people who could throw them in the brig, or worse, demote them, if they got word of it.</p><p>Initially, the pool had been a way to distract themselves of the finality that being stuck in the Delta Quadrant brought with it, along side with the chance of gaining some replicator rations. In those days, their bets were simple, things like: how many times would Captain Janeway touch Commander Chakotay’s shoulder throughout one day?</p><p>After rescuing them from New Earth, the pool turned into a poll. Paris personally asked almost every crewman on board whether they thought the Captain and the Commander had gotten together in their private paradise. Tuvok simply raised an eyebrow at him.</p><p>Of course, sitting at the conn, Paris got to hear firsthand the type of conversations his commanding officers had on a daily basis. They ranged from discussing whatever was attacking them currently, to favorite childhood dishes from home. And then of course, there were the conversation Paris tuned in halfway through, or the out of context bits he heard, which often made him wonder if they knew he was eavesdropping and were messing with him.</p><p>He would never forget the day he heard Captain Janeway congratulate Chakotay on his handy work, telling him how good he made her feel. Paris almost chocked on his own spit, trying to appear as casual as possible and not tense his shoulders. When he told B’Elanna she waved her hand with a snort, telling him the Captain was probably thanking him for a massage, as she often got a stiff neck.</p><p>~*~</p><p>B’Elanna was not one to listen to gossip or fall for them easily. She was well aware a minor fluctuation in sensors became a wormhole by the time it reached the other end of the ship. She definitely did not pay attention to Tom’s wild theories of how the Captain and Chakotay got together on New Earth and kept it secret since, even if she liked to participate in his pool now and then.</p><p>However, she could not deny that something had changed between her commanding officers, and it started after they received their first letters from Starfleet. B’Elanna knew how much Chakotay suffered after learning the news about the Maquis, how much he struggled with the task of having to tell everyone else. She assumed Captain Janeway received equally discouraging news as she spent those days secluded in her Ready Room. It made sense that they would seek refuge and comfort in one another as good friends do.</p><p>But B’Elanna could not help noticing just how close they became after everyone went through their mourning stage. The Captain and Chakotay had always been ones to stand a little closer than regulations required, joke openly on the Bridge, share inside jokes. However, now she was noticing added tenderness to the way Chakotay brought Captain Janeway coffee, how the Captain listened to him talk about his vision quest or to his instructions about talking to her spirit animal. There was a serious note in the Captain’s voice when she instructed Chakotay to be careful on a mission.</p><p>Above all, B’Elanna was taken back by the way their dynamic changed when they were fighting. Neither the Captain nor Chakotay cared about being discreet when having an argument, before, their arguments were measured, to a degree. He knew when not to cross the line, but lately the line seemed to be drawn in sand. Chakotay openly defied Captain Janeway, but not to diminish her authority. It seemed to B’Elanna that he desperately needed to make her see when she was wrong and was endangering the entire crew along with the ship. B’Elanna found it sweet, that he cared so much about the Captain to risk the brig, or worse. Captain Janeway surely did not mind. She would have a special spark in her eyes whenever they argued, and she would walk away with a smirk on her lips.</p><p>~*~</p><p>Harry had been ecstatic when Captain Janeway entrusted him with the night shift. Tom teased him endlessly about it, but he knew his friend was just as proud. Harry really did not mind it, even if sometimes the Gama shift gave him a hard time, trying to slack off while the other senior officers were comfortable in their beds.</p><p>There was one thing he did dislike about the night shift; he could never get a hold of Captain Janeway or Commander Chakotay right away when there was an emergency.</p><p>They did not run into danger often during his watch, and many times consulting Tuvok was enough to solve their issue, but now and then Harry found it appropriate to get his commanding officers. He did not notice it the first couple of times, but after the Ensign at the conn made a comment under her breath, Harry realized she had a point.</p><p>He did not think Commander Chakotay was a heavy sleeper, but every time he called him over the comm system he had to try multiple times to get a response. Usually, it was a grunt and a huff before Chakotay sounded more like himself and gave a coherent answer.</p><p>Once, when Harry just could not get the Commander to answer, he had given up and called Captain Janeway, fists gripping the command chair as he did so. She answered on the first try, but when she stumbled onto the Bridge ten minutes later, messy hair and grumpy face, Harry doubted he had made the right call.</p><p>After leaving the Bridge in the Captain’s hand, whose mood had improved thanks to coffee, Harry headed to his room, but decided to stop by Commander Chakotay’s quarters first to check on him. The captain had not seemed overly concerned when he mentioned that Chakotay did not answer his comm badge. Harry rang the doorbell for a full three minutes before asking the computer to locate the Commander.</p><p>He wished he could forget the “Commander Chakotay is in Captain Janeway’ quarters” response.</p><p>Tom and B’Elanna laughed at him in the mess hall the next day when he asked them why would Chakotay be in the Captain’s rooms late at night.</p><p>Harry realized what it all meant a couple of days latter he walked to his morning shift. He blushed every time either of his commanding officers addressed him that day.</p><p>~*~</p><p>Neelix was sure someone was going through his cabinets in the mess hall. Every Saturday morning, he came in to find a pot of coffee missing, two steel cups, a tray, and other eating utensils gone. Not to mention an array of food, from croissants to strawberries, pancakes, various jams, cheeses, and melted chocolate. He repeatedly asked for added security during meetings with the other senior officers, but Captain Janeway delegated to Commander Chakotay and he seemed to always forget about it. The most infuriating part was that the tray along with the other items, minus the food, would be returned to the mess hall every Sunday, dirty and in a pile on the counter.</p><p>After three months of the same incident, Neelix decided to stake out a watch in the mess hall and catch the thief. He was almost dozing off, sure that the culprit knew he was there and had changed their mind, when the doors to the mess hall swooshed open and closed.</p><p>Neelix was ready to jump out holding his biggest frying pan, when he made out Commander Chakotay’s outline in the partial darkness of the room. He was barefoot, wearing loose sweatpants and a Starfleet issued gray undershirt. He rummaged through Neelix’s kitchen, collecting his supplies as he hummed.</p><p>He sounded almost…happy. Neelix scratched his head as he watched Chakotay leave. He had gathered enough food for two. He blinked.</p><p>“Computer, locate Commander Chakotay.”</p><p>
  <em>Commander Chakotay is in Captain Janeway’s quarters.</em>
</p><p>Neelix blinked at his stove for a few seconds before gasping. Of course, Chakotay had taken food for two! That was breakfast, and almost all of the Captain’s favorite foods.</p><p>He did not mention the Saturday thief in any more crew meetings, but he did smirk at Chakotay when he realized Neelix had dropped the subject.</p><p>~*~</p><p>The Doctor always nagged her about using his ridiculous Holodeck programs to improve her social skills, but Seven was beginning to realize she should just observe Captain Janeway and Commander Chakotay, especially when it came to romantic interactions.</p><p>They were not too obvious with it, in fact, Seven was sure most of the crew had no idea, but she had picked up clues that she had previously gathered information about. It was all in their touches. Not the congratulatory pat on the back the Captain tended to give everyone, but Chakotay the most, but the way she cupped his cheek after a trip to sickbay when the Commander was hurt during a mission. It was in the way Chakotay bounced on the balls of his feet when the Captain returned from a first contact meeting, and how he gripped her forearm while they exited the shuttle bay talking. It was the way they leaned into each-other to whisper during dinners in the mess hall while Neelix prattled on.</p><p>Seven knew that gestures meant as much as words for humans. She assumed that was why Commander Chakotay regularly brought fresh roses to the Captain. Why he brought her coffee in the morning and tea late at night. Why Captain Janeway made sure to swap her cake for his pudding or stop on an inhabited M class planet when they had the time so Chakotay could collect evidence of primate life.</p><p>Seven was inclined to ask Captain Janeway how their relationship had grown so seamlessly, how they were so comfortable with one-another, and if their balance translated well into their sexual encounters, but she had a nagging doubt the Captain would be embarrassed and the Doctor would consider the questions out of line.</p><p>~*~</p><p>Dermal regenerators were in high demand on Voyager as the crew was always getting into minor – and sometimes major – confrontations on their way home so the Doctor was used to people breezing in and out of sickbay asking for one. Usually, it was to treat phaser burns, minor cuts caused by working in Engineering, or the occasional knife cut from one of Neelix’s cooking classes.</p><p>The Doctor started suspecting something when Commander Chakotay visited sickbay asking him to use a dermal regenerator on some bruises along his collarbone. He blamed them on his boxing routine. The next time the bruises were on his neck where his shirt could not cover, and he tried to blame them on the recent away mission. The third time it was apparently from scratching too much. The Doctor just gave him a dermal regenerator to keep, with the added comment that he might be hologram, but he had an extensive database on how bruises were created, and what type of activity caused certain bruises. Commander Chakotay had the decency of blushing at least.</p><p>The Doctor would have forgotten about the entire thing, had it not been for Captain Janeway coming into sickbay with what she called a “personal issue”. The Doctor reminded her that all matters between patient and physician were personal and confidential. He expected an array of issues, or requests, but it did take him back when the Captain asked to restart the reproductive hormone blocker she had stopped after a while of being trapped in the Delta Quadrant.</p><p>The Doctor did not want to pry but he did need to know the reason why, wondering if she were having a hormonal imbalance or irregular period. The Captain stared at her boots when she informed him that she was sexually active and needed to be sure pregnancy did not happen. Since they had been on the ship for months and she had not left on an away mission during the few ones in the time frame, The Doctor did not find it necessary to examine her for alien pathogens. After an injection and a murmured thank you, the Captain left sickbay rather in a hurry.</p><p>It was not until a few days later, while The Doctor was reviewing recent vital signs readings for all crew members who had visited sickbay in order to rule out any mass infection or viruses, that he realized both the Captain’s and Commanders serotonin levels, among other hormones, were elevated. He stared at the screen for quiet a while, weighing if the Captain would delete his program if he called her and Commander Chakotay into sickbay for a safe-sex lesson.</p>
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